BIOMART IMPLEMENTATION OF

SP_BASE

BIOMART IMPLEMENTATION OF

SP_BASEMentors : Andrew Cameron

Peer Mentor:Emmanuella Morin

PI: Eric Davidson

Intern:Steven Hobbs

Mentors : Andrew Cameron

Peer Mentor:Emmanuella Morin

PI: Eric Davidson

Intern:Steven Hobbs

Outline Outline

Background The Project Methods/Approach Future directions

Background The Project Methods/Approach Future directions

Biological significanceBiological significance

The Strongylocentrotus purpuratus is currently a widely used as research model in developmental biology

Sea urchin embryos offer the ability for: The study of cis-regulatory systems Transcription factor isolation Exploration of gene networks

The Strongylocentrotus purpuratus is currently a widely used as research model in developmental biology

Sea urchin embryos offer the ability for: The study of cis-regulatory systems Transcription factor isolation Exploration of gene networks

GMODGMOD

What is GMOD? Generic Model Organism Database a collection of software tools for creating

and managing genome-scale biological databases

What is GMOD? Generic Model Organism Database a collection of software tools for creating

and managing genome-scale biological databases

GoalsGoals

Complete a working online version of Biomart to be used for the purple sea urchin genome

Setup a working public website so that researchers can have easy access to the data

Complete a working online version of Biomart to be used for the purple sea urchin genome

Setup a working public website so that researchers can have easy access to the data

Methods for building a Biomart databaseMethods for building a Biomart database1. Build a relational database to hold the primary

data

2. Alter the database to work with Biomart suite

3. Setup a working public website using Apache that links the Biomart software to the web

4. Alter and maintain the website to be as user-friendly as possible

1. Build a relational database to hold the primary data

2. Alter the database to work with Biomart suite

3. Setup a working public website using Apache that links the Biomart software to the web

4. Alter and maintain the website to be as user-friendly as possible

Data FlowData Flow

MartJAVA

PERL

Source data

DAS

WebGUI

Commandline

Desktop GUI

WebService

Mart builder

Mart editor

Mart runner

Mart view

Data FlowData Flow

MartJAVA

PERL

Source data

DAS

WebGUI

Commandline

Desktop GUI

WebService

Mart builder

Mart editor

Mart runner

Mart view

Data FlowData Flow

MartJAVA

PERL

Source data

DAS

WebGUI

Commandline

Desktop GUI

WebService

Mart builder

Mart editor

Mart runner

Mart view

Data FlowData Flow

MartJAVA

PERL

Source data

DAS

WebGUI

Commandline

Desktop GUI

WebService

Mart builder

Mart editor

Mart runner

Mart view

What is Mart Builder ?What is Mart Builder ?

A program that takes the source data in the form of a database and configures it to be used in other Biomart applications

A program that takes the source data in the form of a database and configures it to be used in other Biomart applications

Mart BuilderMart Builder

Mart editor Mart editor

OUTPUT OUTPUTMart EditorMart Editor

Mart viewMart view

Example demoExample demo

http://www.biomart.org/biomart/martview/e610930b9538b264df6f3467b341a3bf

http://www.biomart.org/biomart/martview/e610930b9538b264df6f3467b341a3bf

Future workFuture work

Linking to other parts of GMOD such as Gbrowse

Connecting to Chado Schema databases

Linking to other parts of GMOD such as Gbrowse

Connecting to Chado Schema databases

Acknowledgements:Acknowledgements:

SP_base project team

CalState LA /SoCal BSI

Davidson Lab at Caltech

Andrew Cameron, Ph.D

Funding was provided by:

NSF(National Science foundation)

NIH(National institute of Health)

Economic & Workforce development

SP_base project team

CalState LA /SoCal BSI

Davidson Lab at Caltech

Andrew Cameron, Ph.D

Funding was provided by:

NSF(National Science foundation)

NIH(National institute of Health)

Economic & Workforce development